You're extrapolating more from the verse than necessary. It doesn't say that a halachic sukkah should be protection from storm and rain. It's also not even talking about a sukkah that you sit in during Sukkos.
Let's see the verse which precedes this one (Chabad translation):
וּבָרָ֣א יְהֹוָ֡ה עַל֩ כָּל־מְכ֨וֹן הַר־צִיּ֜וֹן וְעַל־מִקְרָאֶ֗הָ עָנָ֚ן | יוֹמָם֙ וְעָשָׁ֔ן וְנֹ֛גַהּ אֵ֥שׁ לֶֽהָבָ֖ה לָ֑יְלָה כִּ֥י עַל־כָּל־כָּב֖וֹד חֻפָּֽה:
And the Lord shall create over every dwelling of Mount Zion and over all those summoned therein, a cloud by day and smoke, and splendor of a flaming fire at night, for, in addition to every honor, there will be a shelter.
So it's discussing that Hashem will create a cloud for shelter.
Then it immediately starts discussing a sukkah that will protect. A sukkah is literally a covering, and in context the verse would seem to be referring to this cloud as a sukkah. This cloud will protect them from storm and rain. The Rashash (end of Sukkah 2a) says this is the simplest understanding of the verse.
Even if you disagree that the verse isn't talking about the cloud, it's not perforce that it's telling you anything about a halachic sukkah. While there is an opinion in the gemarra that it is, this would seem to be on the level of derash, not peshat. Indeed, those that disagree with him there say the verse is talking about a Messianic sukkah (as is clear from the context), not a halachic sukkah. Just because that sukkah will protect from storm and rain, you don't see anything about the sukkos we sit in today.
The gemarra in Bava Basra even says that in the future Hashem will make a sukkah with sechach from the hide of the Leviasan. I don't have a source but perhaps it's the same sukkah as your verse. It's not so simple that that sukkah will be kosher for Sukkos...so again we see Messianic sukkos aren't relevant to today.